Question about computeGCbias plot

[Jennifer Ishii]

Hi

I am new to deeptools and so far its great - thanks for making it available!

I ran a computeGCBias analysis on both my pulldown and input samples. I would like to set the Y-axes to the same max for consistency but I cannot find a way to adjust the plot parameters on deeptools. 

Is it possible to adjust plot parameters in Galaxy?

If not, how can I obtain the data used to generate the plot so that I can re-graph locally?

Thanks for your help,

Best,

Jennifer

[Friederike Dündar]

Hi Jenny,

thanks for identifying this gap in our documentation - computeGCbias outputs the frequency table that underlies the image that is generated and I suggest you use that text file to generate the plots you envision. However, we have pretty much neglected spelling out what that frequency table actually contains (I also had to look it up in the code, and infer from there) - sorry about that.

Each row of that table corresponds to one bin representing the 300 bp fragments of the genome with a certain GC fraction. The rows are sorted from 0% GC to 100% GC. The first column contains the observed number of reads per GC bin, the second column the expected number of reads per GC bin and the third column contains the ratio of observed/expected normalized for sequencing depth.

So, you can take that frequency table and simply plot the values of the 3rd column. Note that the original deepTools output will show you the log2-transformed values of the third column, so you may want to log2-transform them as well, centering the plot around 0.

Hope that helps!

Best,

Friederike

--
You received this message because you are subscribed to the Google Groups "deepTools" group.
To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.